rs3198697
This is a synonymous variant in the PDXDC1 gene — it does not change the protein's amino acid sequence.
▶GWAS Catalog Trait Associations (10)
Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.
GWAS Catalog Trait Associations (10)
Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.
cholesteryl ester 20:3 measurement
Harshfield EL et al. “Genome-wide analysis of blood lipid metabolites in over 5000 South Asians reveals biological insights at cardiometabolic disease loci.” Bmc Medicine 19(1):232 (2021)
Allele T
OR 0.14
p 4.0e-43
N 13,814
Large GWAS
European
fatty acid amount
Harshfield EL et al. “Genome-wide analysis of blood lipid metabolites in over 5000 South Asians reveals biological insights at cardiometabolic disease loci.” Bmc Medicine 19(1):232 (2021)
Allele T
OR 0.06
p 3.0e-13
N 13,814
Large GWAS
European
Richardson TG et al. “Characterising metabolomic signatures of lipid-modifying therapies through drug target mendelian randomisation.” Plos Biology 20(2):e3001547 (2022)
Allele T
OR 0.03
p 1.0e-10
N 115,006
Large GWAS
European
level of phosphatidylethanolamine
Harshfield EL et al. “Genome-wide analysis of blood lipid metabolites in over 5000 South Asians reveals biological insights at cardiometabolic disease loci.” Bmc Medicine 19(1):232 (2021)
Allele T
OR 0.05
p 2.0e-11
N 13,814
Large GWAS
European
polyunsaturated fatty acid measurement
Sun Y et al. “GWAS and multi-omics integrative analysis reveal novel loci and their molecular mechanisms for circulating fatty acids.” Hgg Advances 6(4):100470 (2025)
Allele T
OR —
p 2.0e-11
N 128,922
Large GWAS
European
triglycerides in large HDL measurement
Karjalainen MK et al. “Genome-wide characterization of circulating metabolic biomarkers.” Nature 628(8006):130-138 (2024)
Allele T
OR 0.03
p 5.0e-10
N 136,016
Large GWAS
multi-ancestry
monounsaturated fatty acids; 16:1, 18:1 measurement
Davyson E et al. “Metabolomic Investigation of Major Depressive Disorder Identifies a Potentially Causal Association With Polyunsaturated Fatty Acids.” Biological Psychiatry 94(8):630-639 (2023)
Allele T
OR 0.03
p 1.0e-9
N 88,268
Large GWAS
European
insomnia
Watanabe K et al. “Genome-wide meta-analysis of insomnia prioritizes genes associated with metabolic and psychiatric pathways.” Nature Genetics 54(8):1125-1132 (2022)
Allele T
OR 0.01
p 3.0e-9
N 1,409,137
Meta-analysisLarge GWAS
European
free cholesterol:total lipids ratio, intermediate density lipoprotein measurement
Richardson TG et al. “Characterising metabolomic signatures of lipid-modifying therapies through drug target mendelian randomisation.” Plos Biology 20(2):e3001547 (2022)
Allele C
OR 0.02
p 6.0e-9
N 115,082
Large GWAS
European
level of phosphatidylcholine
Harshfield EL et al. “Genome-wide analysis of blood lipid metabolites in over 5000 South Asians reveals biological insights at cardiometabolic disease loci.” Bmc Medicine 19(1):232 (2021)
Allele T
OR 0.07
p 5.0e-14
N 13,814
Large GWAS
European
triglyceride measurement
Hoffmann TJ et al. “A large electronic-health-record-based genome-wide study of serum lipids.” Nature Genetics 50(3):401-413 (2018)
Allele C
OR —
β 0.028
p 8.0e-11
N 94,674
Large GWAS
multi-ancestry
Willer CJ et al. “Discovery and refinement of loci associated with lipid levels.” Nature Genetics 45(11):1274-1283 (2013)
Allele C
OR —
β 0.020
p 2.0e-8
N 94,595
Large GWAS
European
▶ClinVar annotation
About PDXDC1
Enables cadherin binding activity. Predicted to be involved in carboxylic acid metabolic process. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Jul 2025]
View all PDXDC1 variants →Gene information from NCBI Gene. Variant classifications from ClinVar.
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